Concept 3.3: Some Proteins Act as Enzymes to Speed up Biochemical Reactions

In Chapter 2 we introduced the concepts of biological energetics. We showed that some metabolic reactions are exergonic and some are endergonic, and that biochemistry obeys the laws of thermodynamics (see Figures 2.14 and 2.15). Knowing whether energy is supplied or released in a particular reaction tells us whether the reaction can occur in a living system. But it does not tell us how fast the reaction will occur.

Living systems depend on reactions that occur spontaneously. But without help, most of these reactions would proceed at such slow rates that an organism could not survive. The role of a catalyst is to speed up a reaction without itself being permanently altered. A catalyst does not cause a reaction to occur, but it increases the rate of the reaction. This is an important point: No catalyst makes a reaction occur that would not proceed without it.

Biological catalysts are called enzymes; for example, the synthesis of prostaglandin (see the opening story) is catalyzed by an enzyme (cyclooxygenase). Most enzymes are proteins, but a few important enzymes are RNA molecules called ribozymes. An enzyme can bind the reactants in a chemical reaction and participate in the reaction itself. However, this participation does not permanently change the enzyme. At the end of the reaction, the enzyme is unchanged and available to catalyze additional, similar reactions.

An energy barrier must be overcome to speed up a reaction

An exergonic reaction releases free energy (G), which is the amount of energy in a system that is available to do work. For example, the free energy released in an exergonic reaction can be used by the cell to drive an endergonic reaction, or it can be converted to mechanical energy for movement (see Figure 6.1). But without a catalyst, a reaction will usually take place very slowly. This is because there is an energy barrier between the reactants and the products. Think about the hydrolysis of sucrose, which we described in Concept 2.5.

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Sucrose + H2O → glucose + fructose

In humans, this reaction is part of the process of digestion. The reaction is exergonic, but even if water is abundant, the sucrose molecule will only rarely bind the H atom and the —OH group in the water molecule at the appropriate locations to break the covalent bond between the glucose and fructose—unless there is an input of energy to initiate the reaction. Such an input of energy will place the sucrose into a reactive mode called the transition state. The energy input required for sucrose to reach this state is called the activation energy (Ea). Once the transition state is reached, the reaction can proceed spontaneously with a release of free energy (ΔG is negative) (FIGURE 3.12A). The image of a ball rolling over a bump and then down a hill helps illustrate these concepts (FIGURE 3.12B).

Figure 3.12: Activation Energy Initiates Reactions (A) In any chemical reaction, an initial stable state must become less stable before change is possible. (B) A ball on a hillside provides a physical analogy to the biochemical principle graphed in A. Although these graphs show an exergonic reaction, activation energy is needed for endergonic reactions as well.

Where does the activation energy come from? In any collection of reactants at room or body temperature, the molecules are moving around. Recall from Chapter 2 that the energy the molecules possess due to this motion is called kinetic energy. A few molecules are moving fast enough that their kinetic energy can overcome the energy barrier; they enter the transition state and react. So the reaction takes place—but very slowly. If the system is heated, all the reactant molecules have more kinetic energy, and the reaction speeds up. You have probably used this technique in the chemistry laboratory.

Adding enough heat to increase the average kinetic energy of the molecules would not work in a living system, however. Such a nonspecific approach would accelerate all reactions, including destructive ones such as the denaturation of proteins.

An enzyme lowers the activation energy for a reaction by enabling the reactants to come together and react more easily; the reactants need lower amounts of kinetic energy to enter their transition states (FIGURE 3.13). In this way, an enzyme can change the rate of a reaction substantially. For example, if a molecule of sucrose just sits in solution, hydrolysis may take hundreds of years. But with the enzyme sucrase present, the same reaction occurs in 1 second! Typically, an enzyme-catalyzed reaction proceeds 103 to 108 times faster than the uncatalyzed reaction, and the enzyme converts 100 to 1,000 substrate molecules into product per second.

Figure 3.13: Enzymes Lower the Energy Barrier The activation energy (Ea) is lower in an enzyme-catalyzed reaction than in an uncatalyzed reaction, but the free energy released is the same with or without catalysis. A lower activation energy means the reaction will take place at a faster rate.

Go to ACTIVITY 3.4 Free Energy Changes

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Enzymes bind specific reactants at their active sites

Catalysts increase the rates of chemical reactions. Most nonbiological catalysts are nonspecific. For example, powdered platinum catalyzes virtually any reaction in which molecular hydrogen (H2) is a reactant. In contrast, most biological catalysts are highly specific. An enzyme usually recognizes and binds to only one or a few closely related reactants, and it catalyzes only a single chemical reaction.

In an enzyme-catalyzed reaction, the reactants are called substrates. Substrate molecules bind to a particular site on the enzyme, called the active site, where catalysis takes place (FIGURE 3.14). The specificity of an enzyme results from the exact three-dimensional shape (also called conformation) and chemical properties of its active site. Only a narrow range of substrates, with specific shapes, functional groups, and chemical properties, can fit properly and bind to the active site. The names of enzymes reflect their functions and often end with the suffix “ase.” For example, the enzyme sucrase catalyzes the hydrolysis of sucrose, and we write the reaction as follows:

Figure 3.14: Enzyme Action Sucrase catalyzes the hydrolysis of sucrose. After the reaction, the enzyme is unchanged and is ready to accept another substrate molecule.

The binding of a substrate (S) to the active site of an enzyme (E) produces an enzyme–substrate complex (ES) that is held together by one or more means, such as hydrogen bonding, ionic attraction, or temporary covalent bonding. The enzyme–substrate complex gives rise to product (P) and free enzyme:

E + S → ES → E + P

(As we have seen in the case of sucrase, a single enzyme-catalyzed reaction may involve multiple substrates and/or products.) The free enzyme (E) is in the same chemical form at the end of the reaction as at the beginning. While bound to the substrate(s), it may change chemically, but by the end of the reaction it has been restored to its initial form and is ready to catalyze the same reaction again (see Figure 3.14).

How Enzymes Work

During and after the formation of the enzyme–substrate complex, chemical interactions occur. These interactions contribute directly to the breaking of old bonds and the formation of new ones. In catalyzing a reaction, an enzyme may use one or more mechanisms:

The active site is usually only a small part of the enzyme protein. But its three-dimensional structure is so specific that it binds only one or a few related substrates. The binding of the substrate to the active site depends on the same relatively weak forces that maintain the tertiary structure of the enzyme: hydrogen bonds, the attraction and repulsion of charged groups, and hydrophobic interactions. Scientists used to think of substrate binding as being similar to a lock and key fitting together. Actually, for most enzymes and substrates the relationship is more like a baseball and a catcher’s mitt: the substrate first binds, and then the active site changes slightly to make the binding tight. FIGURE 3.15 illustrates this “induced fit” phenomenon. (We introduced the concept of protein structure changes earlier; see Figure 3.11.)

Figure 3.15: Some Enzymes Change Shape When Substrate Binds to Them Shape changes result in an induced fit between enzyme and substrate, improving the catalytic ability of the enzyme. Induced fit can be observed in the enzyme hexokinase, seen here with and without its substrates, glucose (green) and ATP (yellow).

Induced fit at least partly explains why enzymes are so large. The rest of the macromolecule has at least three roles:

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Nonprotein Partners for Enzymes

Some enzymes require ions or other molecules in order to function. These molecules are referred to as cofactors, and they can be grouped into three categories (TABLE 3.3):

Some Examples of Enzyme Cofactors

Rate of Reaction

The rate of an uncatalyzed reaction is directly proportional to the concentration of the substrate. The higher the concentration, the more reactions per unit of time. As we have seen, the addition of the appropriate enzyme speeds up the reaction, but it also changes the shape of the plot of rate versus substrate concentration (FIGURE 3.16). For a given concentration of enzyme, the rate of the enzyme-catalyzed reaction initially increases as the substrate concentration increases from zero, but then it levels off.

Figure 3.16: Catalyzed Reactions Reach a Maximum Rate Because there is usually less enzyme than substrate present, the reaction rate levels off when the enzyme becomes saturated.

Why does this happen? The concentration of an enzyme is usually much lower than that of its substrate and does not change as substrate concentration changes. When all the enzyme molecules are bound to substrate molecules, the enzyme is working at its maximum rate. Under these conditions the active sites are said to be saturated.

The maximum rate of a catalyzed reaction can be used to measure how efficient the enzyme is—that is, how many molecules of substrate are converted into product by an individual enzyme molecule per unit of time, when there is an excess of substrate present. This turnover number ranges from 1 molecule every second for sucrase to an amazing 40 million molecules per second for the liver enzyme catalase.

CHECKpoint CONCEPT 3.3

  • Explain how the structure of an enzyme makes that enzyme specific.
  • What is activation energy? How does an enzyme lower the activation energy needed to start a reaction?
  • Compare coenzymes with substrates. How do they work together in enzyme catalysis?
  • Compare the state of an enzyme active site at a low substrate concentration and at a high substrate concentration. How does this affect the rate of the reaction?

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Now that you understand more about how enzymes function, let’s see how different enzymes work in the metabolism of living organisms.